Vanuatu has defended a boycott of the Melanesian Spearhead Group (MSG) foreign minister's mission to Indonesia.

The joint delegation was agreed to at last year's MSG leader's summit in New Caledonia, with the purpose of the meeting being to examine the status of the province of Papua, a mainly Melanesian and Christian part of Indonesia comprising the western half of the island of New Guinea.

Vanuatu's Foreign Minister, Edward Natapei, has told Radio Australia's Pacific Beat he believes the agenda for the foreign minister's meeting had been "hijacked" by Indonesia.

Mr Natapei says it was made clear to the MSG leaders and the Indonesian government that Vanuatu would only participate if the delegation was given the opportunity to meet civil society groups, pro-independence groups, church leaders and other groups concerned with alleged human rights violations in West Papua.

"Just one day before we were to depart Vanuatu to travel to Indonesia, we got the program of the visit, which neglected, it did not involve a meeting with civil society, it did not involve a meeting with the West Papuan people, the leadership in West Papua," he said.

"We realised that in fact it was being hijacked by the government of Indonesia to work on another issue, which was to promote economic ties and development cooperation with the government of Indonesia."

The delegation was also tasked with assessing what support there was from indigenous groups there for the Vanuatu-based West Papua National Coalition for Liberation to be given MSG membership.

The MSG brings together the leaders of Fiji, Papua New Guinea, Solomon Islands and Vanuatu, along with New Caledonia's indigenous political movement FLNKS.

West Papuan activists see membership of the MSG as a step towards international recognition.

Decision commended

The agenda for the mission included the signing of a trade agreement, with less than a day to be spent in Papua.

The West Papua Liberation movement has commended the Vanuatu government's decision to boycott the visit.

The vice chairman of the West Papua National Coalition for Liberation, John Ondawame, says he's disappointed the MSG mission is not getting the chance spend more time in Papua.

"Stay[ing] only half day in Jayapura without meeting with affected people, particularly [the] resistance movement, the church leaders, tribal councils, women's organisations, the civil society at large.

"This says so clearly to the world that Indonesia is not serious [about] with requests by the MSG, but the Indonesian agenda - not to allow any MSG [foreign] ministers... to visit West Papua to monitor the current situation on the ground.

There are reports that more then 40 West Papuans were arrested during the MSG in Jayapura, either of people who tried to contact the MSG group or protested when the MSG delegates arrived at the airport.

Mr Ondawame says this is an indication of Indonesia's "true colours" as a "colonial power".

"[It will] become clear that Indonesia kills or suppresses people on the ground that want for political change," he said.

Divided opinion

Mr Natapei says the MSG is split over the issue of membership for the West Papua Liberation Movement, and says it's now unlikely the West Papuan separatist group will be admitted to the MSG as a full member.

But the Vanuatu government's special envoy, MP Joe Natuman, says his government won't be part of it, and any agreement signed in Jakarta between other Melanesian nations and Indonesia will have to be on an individual basis rather than on behalf of the MSG.

However, he says Vanuatu won't give up on its efforts to have the West Papuans admitted.

"Vanuatu is still going to push...(the) agenda forward," he said.

Mr Natuman says any agreement signed in Jakarta between other Melanesian nations and Indonesia will have to be on an individual basis rather than on behalf of the MSG.

"Because I think there will be a signing, according to this program, a joint statement to be issued by the Republic of Indonesia and also the Melanesian Spearhead Group... they will be signing this statement which has nothing to do with what we've agreed," he said.

"It has everything to do with Jakarta developing its economic ties."

Support within Vanuatu

Support for the plight of the West Papuan independence movement has grown in Vanuatu.

Editor of the Vanuatu Independent, Tony Wilson, says Prime Minister Moana Carcasses' strong position on the issue since he came to power last March has resonated with the Ni-Vanuatu public.

"It's something that's been very much a part of the leadership of the current Prime Minister," he said.

"At one stage late last year he even took the opportunity during a visit to the United Nations in New York to strongly talk about the future plans for West Papua and possible independence.

"His attitude and strong stance has met a real chord with the people here in Vanuatu."

Mr Wilson says the current mission to Indonesia is unlikely to give the attending MSG member representatives any further understanding of whether the West Papua National Coalition for Liberation represents the people in Papua, and whether the group has their backing.

"As it stands though the government here is still strongly supporting this particular group and are rallying behind their application to join the MSG, and I think ultimately they'll push for that membership," he said.

"I know there's some opposition, particularly from Fiji, but this particular mission is exactly what they said it was going to be here.

"It was the Indonesian authorities showing the MSG leaders exactly what they wanted them to see."

The MSG Secretariat has refused to comment on Vanuatu's dismissal of the Indonesian trip, saying it does not comment on the position or policies of its members.